That would certainly be better than nothing.
But, it takes a lot more than a spray can primer to properly protect metal.
First, primers are much more porous than top coats. And provide very limited corrosion protection. If you have ever seen a car where someone sanded a bunch of spots and just primered them, at some point, the rust stains eventually start showing as rust comes right through every primer spot. This is because its not a good moisture barrier, by it's self.
Secondly, drill holes create very sharp edges. And, sharp edges are very difficult to build paint film up on. You can see this, by taking something like a lawn mower blade and trying to paint the sharpened edge. No matter how much paint you spray at it, it moves off the sharp edge. So, even if you carefully paint each hole, (and I have sprayed a ton of them), you still have very little film build on the sharp edge, on each side of the hole. So, you still only have a slight amount of corrosion protection.
When parts are stamped, care is taken to avoid creating sharp edges, so they don't have the same problem. They also use electrostatic spray equipment, that causes paint to be applied more evenly more.
Believe me, I have tried everything imaginable on these holes over the years.
The most effective thing I have found, which was still limited, is window weld primer. This product is designed to protect the metal under your glass, when it's glued in.
3M Single Step Primer 8682
As I said, I hope the rustproofers have found an actual solution to this problem.
If not, personally, I would not allow any holes drilled in my car.